Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes

Abstract

The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes covering the three domains of life makes it possible to contrast these predictions with empirical data. We performed a systematic analysis of the phylogenetic relationships of ancestral eukaryotic genes with archaeal and bacterial genes. In contrast with previous studies, we emphasize the critical importance of methods accounting for statistical support, horizontal gene transfer, and gene loss, and we disentangle the processes underlying the phylogenomic pattern we observe. We first recover a clear signal indicating that a fraction of the bacteria-like eukaryotic genes are of alphaproteobacterial origin. Then, we show that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group. We also provide evidence that eukaryotes branch close to the last archaeal common ancestor. Our results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria. Overall, they leave only two possible interpretations, respectively, based on the early-mitochondria hypotheses, which suppose an early endosymbiosis of an alphaproteobacterium in an archaeal host and on the slow-drip autogenous hypothesis, in which early eukaryotic ancestors were particularly prone to horizontal gene transfers.

Keywords: archaea; eukaryogenesis; evolution; horizontal gene transfer; phylogeny; tree of life.

Fig. 1.

Gene trees were examined by means of configurations. (A) Schematic diagrams of six archetypal configurations. (B–D) Examples. The taxonomic sampling is always that of table 1. The numbers on branches represent nonparametric bootstrap supports (values below 50% are not shown). (B) ML tree of the hydroxybenzoate polyprenyltransferase (COQ2) LECA clade, which was annotated as “alphaproteobacteria-related.” The node at the base of the stem of eukaryotes, which NBS support was 62%, is marked by a black circle. (C) ML tree of the “long-chain acyl-CoA ligase” LECA clade. The sister group of eukaryotes consisted of an isolated M. xanthus sequence, which is likely the result of a recent HGT as most of the seven other Deltaproteobacteria do not encode related sequences. Therefore, this LECA clade was annotated as bacterial-domain-related (related to bacteria, but not to any phylum in particular). (D) ML tree of the “4-nitrophenylphosphatase” LECA clade, annotated as unclear because archaeal (in green) and bacterial (in black) sequences were mixed.

Fig. 2.

Inferred prokaryotic origins of eukaryotic genes. Each row represents 1 of 434 LECA clades and reports, from left to right, the configuration of its ML tree (the color code is given by the legend, top), the local topological support (“Sup.” column; NBS and SGS are in black and gray, respectively), and the configurations that appear in bootstrap trees. LECA clades are sorted by configurations and decreasing node support. A “R” letter on the right indicates that the gene is encoded in the mitochondrial genome in R. americana. Overall, 41 LECA clades were traceable to Alphaproteobacteria (pink), 24 to other bacterial phyla, among which 3 were so with high support values (arrows, and see Results), 177 to Bacteria though not to a particular taxonomic group (bacterial-domain-related, deep blue), while three appeared in the three-domain (3D) configuration (black), 117 were related to Archaea (green), and 71 were of unclear origin (white).

Fig. 3.

Ability of our approach to recover the alphaproteobacterial origin of mitochondrially encoded genes. Fourteen LECA clades (among 434) corresponded to genes that are encoded in the mitochondrial genome in R. americana. Figure is to be read like figure 2, except that LECA clades are sorted by decreasing (SGS, gray) support values. LECA clades having SGS values higher than 45% (dashed line) could be traced to Alphaproteobacteria, but those with lower supports could not, due to a lack of phylogenetic signal. For the third and eighth LECA clades from top (arrows), association with Alphaproteobacteria was weaker because of HGTs from Alphaproteobacteria to Magnetococcus marinus and Gammaproteobacteria, respectively.

Fig. 4.

The missing support for the monophyly of Archaea. Histogram of bootstrap supports for the monophyly of Archaea and Bacteria in 28 nearly universal clusters of homologs. Although the monophyly of Bacteria was strongly recovered, that of Archaea was not, illustrating the fragility of the archaeal “domain” and the intimate relationship between Eukarya and Archaea.

Fig. 5.

The impact of configurations on the determination of the origins of ancestral eukaryotic genes. The diagrams represent the origins of 434 LECA clades as inferred from their ML trees using (A) configurations or (B) the simpler but naive sister-clade-identity criterion. The colors correspond to the legend given in figure 2. Labels corresponding to fewer than five LECA clades were omitted. The sister-clade-identity criterion was overconfident regarding vertical inheritance and generated many spurious annotations. In contrast, configurations conservatively interpret the phylogenies where peculiar taxonomic distributions suggest HGTs, like in figure 1C. See supplementary figure S5, Supplementary Material online, for a more detailed comparison.